Contacts of the helix formed by residues 334 - 348 (chain F) in PDB entry 1D0A
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 334 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F MET* 1.3 62.8 + - - +
336F ALA* 3.2 3.2 - - - +
337F ASP* 3.4 24.2 - - + +
338F LEU* 2.6 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 335 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E LEU* 5.5 2.9 - - - +
334F ALA* 1.3 81.7 - - - +
336F ALA* 1.3 59.2 + - + +
338F LEU* 4.5 2.3 - - - +
339F GLU* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F ALA 4.4 1.2 - - - +
335F MET* 1.3 77.7 - - + +
337F ASP* 1.3 65.4 + - - +
338F LEU 3.4 0.4 - - - -
339F GLU* 3.4 9.8 + - - +
340F GLN* 3.3 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F ALA* 3.1 23.9 + - + +
336F ALA* 1.3 79.7 - - - +
338F LEU* 1.3 60.7 + - - +
340F GLN* 3.2 19.8 + - - +
341F LYS* 3.5 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D MET 4.3 11.4 - - - +
338D LEU* 5.2 7.4 - - + -
339D GLU* 4.2 30.5 - - + +
342D VAL* 4.5 22.2 - - + -
343D LEU* 6.0 2.9 - - + -
338E LEU* 4.7 14.1 - - + -
334F ALA* 2.6 22.4 + - + +
335F MET* 4.5 2.9 - - - +
337F ASP* 1.3 71.7 - - - +
339F GLU* 1.3 63.4 + - - +
340F GLN 3.1 0.7 - - - -
341F LYS* 3.1 23.8 + - + -
342F VAL* 3.3 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E LEU* 4.3 22.4 - - + +
335F MET 3.6 14.6 + - - +
336F ALA* 3.4 14.5 + - - +
337F ASP 3.2 0.2 - - - -
338F LEU* 1.3 77.8 - - - +
340F GLN* 1.3 58.7 + - - +
342F VAL* 3.4 4.5 + - - +
343F LEU* 3.1 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F ALA 3.3 8.3 + - - +
337F ASP* 3.2 12.7 + - - +
338F LEU 3.1 0.6 - - - -
339F GLU* 1.3 78.7 - - - +
341F LYS* 1.3 59.4 + - - +
343F LEU* 3.5 11.5 - - + +
344F GLU* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 341 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D VAL* 4.7 7.4 - - + -
343D LEU* 6.6 0.2 - - + -
346D GLU* 5.4 5.5 - - - +
337F ASP 3.5 4.6 + - - +
338F LEU* 3.1 28.0 + - + +
340F GLN* 1.3 80.3 - - - +
342F VAL* 1.3 59.3 + - - +
344F GLU* 3.4 5.6 + - - +
345F MET* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D VAL* 3.8 30.7 - - + -
338E LEU* 3.7 33.7 - - + -
341E LYS* 4.6 5.8 - - + -
342E VAL* 4.2 11.4 - - + -
345E MET* 3.9 22.9 - - + +
338F LEU* 3.3 12.0 + - + +
339F GLU 3.8 7.0 - - - +
341F LYS* 1.3 75.0 - - - +
343F LEU* 1.3 67.1 + - + +
345F MET* 3.4 9.1 + - - +
346F GLU* 3.0 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E LEU* 6.5 0.4 - - + -
339F GLU* 3.1 20.5 + - + +
340F GLN* 3.5 11.9 - - + +
341F LYS 3.2 0.2 - - - -
342F VAL* 1.3 79.6 - - + +
344F GLU* 1.3 60.9 + - - +
346F GLU* 3.2 36.5 + - - +
347F ALA* 3.3 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F GLN 2.8 17.6 + - - +
341F LYS* 3.8 6.5 - - - +
343F LEU* 1.3 74.5 - - - +
345F MET* 1.3 65.7 + - + +
347F ALA* 3.3 5.7 + - - +
348F SER* 3.1 23.4 + - - -
379F PRO* 5.3 7.6 - - + +
380F ALA* 4.8 7.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 345 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D VAL* 3.3 35.7 - - + +
345D MET* 3.7 22.4 - - + +
346D GLU* 3.4 52.9 - - + +
345E MET* 3.9 11.4 - - + +
385E ARG* 5.0 0.3 + - - -
341F LYS 2.9 21.3 + - - +
342F VAL* 3.7 7.4 - - - +
344F GLU* 1.3 77.8 - - + +
346F GLU* 1.3 63.1 + - - +
348F SER* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E LYS* 5.2 6.9 - - - +
345E MET* 3.6 29.8 - - + +
350E TYR* 5.3 2.3 + - - -
385E ARG* 3.2 19.1 + - - -
342F VAL* 3.0 15.7 + - - +
343F LEU* 3.2 35.0 - - - +
345F MET* 1.3 77.8 - - - +
347F ALA* 1.3 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E ARG* 3.8 4.3 + - - +
386E TYR* 4.5 1.2 + - - -
343F LEU 3.3 8.7 + - - +
344F GLU 3.3 3.1 + - - +
345F MET 3.2 0.6 - - - -
346F GLU* 1.3 78.4 - - + +
348F SER* 1.3 65.5 + - - +
349F THR* 3.7 5.5 + - - +
354F PHE* 3.3 24.3 - - + -
379F PRO* 3.6 34.3 - - + -
380F ALA 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E ARG* 3.1 18.9 + - - -
344F GLU 3.1 13.6 + - - -
345F MET* 2.9 25.1 + - - +
347F ALA* 1.3 76.6 - - - +
349F THR* 1.3 59.8 + - - +
350F TYR* 3.6 30.0 + - - -
380F ALA 3.5 17.7 + - - -
382F TYR* 4.2 9.6 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il